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- PDB-8rxl: TEAD2 with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8rxl
TitleTEAD2 with an inhibitor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / inhibitor / complex
Function / homology
Function and homology information


TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis ...TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / sequence-specific double-stranded DNA binding / disordered domain specific binding / protein-containing complex assembly / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / : / YAP binding domain
Similarity search - Domain/homology
: / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGuichou, J.F. / Gelin, M. / Allemand, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: TEAD2 with an inhibitor
Authors: Guichou, J.F. / Gelin, M. / Allemand, F.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transcriptional enhancer factor TEF-4
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5895
Polymers54,9102
Non-polymers6793
Water34219
1
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8403
Polymers27,4551
Non-polymers3852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7482
Polymers27,4551
Non-polymers2931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.922, 61.651, 80.111
Angle α, β, γ (deg.)90.00, 117.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2


Mass: 27455.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15562
#2: Chemical ChemComp-A1H3Z / 4-(5-phenylmethoxy-1~{H}-indol-3-yl)butan-2-one


Mass: 293.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9697 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 2.29→48.45 Å / Num. obs: 21606 / % possible obs: 88.09 % / Redundancy: 2 % / CC1/2: 0.91 / CC star: 0.976 / Net I/σ(I): 14.71
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 1714 / CC1/2: 0.797 / CC star: 0.942

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.36 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27061 1058 5 %RANDOM
Rwork0.20829 ---
obs0.21151 20091 88.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.19 Å2
2--0.36 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.29→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 50 19 3386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193460
X-RAY DIFFRACTIONr_bond_other_d0.0020.023245
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9614675
X-RAY DIFFRACTIONr_angle_other_deg0.93137419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7595399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34922.768177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07115573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.361531
X-RAY DIFFRACTIONr_chiral_restr0.0790.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023864
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02891
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4946.4731611
X-RAY DIFFRACTIONr_mcbond_other4.4966.4711610
X-RAY DIFFRACTIONr_mcangle_it6.9069.6822002
X-RAY DIFFRACTIONr_mcangle_other6.9049.6842003
X-RAY DIFFRACTIONr_scbond_it5.1147.1311849
X-RAY DIFFRACTIONr_scbond_other5.1127.1321850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.06710.4742673
X-RAY DIFFRACTIONr_long_range_B_refined11.4452.6093624
X-RAY DIFFRACTIONr_long_range_B_other11.43752.6173623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å
RfactorNum. reflection% reflection
Rfree0.349 62 -
Rwork0.34 1171 -
obs--70.3 %

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